Shotgun microbial profiling of fossil remains
Shotgun microbial profiling of fossil remains
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DOI：
10.1111/mec.12690
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发表时间：
2014-04-01
影响因子：
4.9
通讯作者：
Orlando, L.
中科院分区：
文献类型：
--
作者：
Der Sarkissian, C.;Ermini, L.;Orlando, L.
由于下一代测序平台的大规模生产，现在可以从古代骨骼遗骸中生成数百万到数十亿的DNA序列。除了特殊的内源性DNA保存情况外，从化石材料中分离出的大多数序列并不来自感兴趣的标本，而是反映了死后在标本上定居的环境生物。在这里，我们的特点是微生物多样性恢复从七个C。200-从北方西伯利亚采集的13000年前的马骨。我们使用一个强大的，基于分类学的分配方法来识别存在于古代DNA提取物中的微生物，并量化它们的相对丰度。我们的研究结果表明，分子保存壁龛存在于古老的样本，可以潜在地用于表征的环境中的遗骸被回收。此外，7个样本的微生物群落分析揭示了特定地点的环境特征。这些微生物群落似乎主要由最近在化石上定居的生物组成。我们的方法显着扩展了使用鸟枪测序方法可以从古代标本中恢复的有用数据量。在未来，有可能将例如死后DNA损伤的积累与特定微生物的存在和/或丰度相关联。
Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.